Photon lists within TIFF files

[Terry L. Sprout]

Hello,

 

I write scientific imaging software, which writes TIFF files to archive
images. I recently added the ability to locate single photons in an
image to sub-pixel accuracy. The software then uses the list of photons
to create a new image that can be integrated for long exposures. When
archiving these images, we only want to archive the list of photons and
not the 2D image that is usually included in a TIFF file.

 

I came up with a scheme that uses an IFD tag that I registered with
Adobe. I want other TIFF readers to be able to use these files as well.

 

I know others must have done this before and it might be best if I
conform to existing schemes to make my files readable by other TIFF
readers. Does anyone know of a scheme that is already being used? Is
there an ImageJ plug-in for reading such files?

 

I don't know much about what can be done with ImageJ. Can a developer
extend the file formats used by ImageJ? In other words, can I write a
plug-in to read these files of should someone from NIH extend the TIFF
reader to read these files?

 

 

Terry L. Sprout

[phone]

w7-32

 

[Frederic V. Hessman]

This is a classic example of what FITS tables give you.  

You all may know of the simple FITS images supported by ImageJ, but the standard actually supports much more complex data, including tabular data (both as text and binary).   For example, most X-ray telescopes use FITS tables, since their proportional counters do exactly what you're doing: counting individual photons, their positions, and the times.  The pixelation scheme called HEALPIX (which covers a sphere with equal area diamonds at various resolutions) used by all-sky surveys like WMAP (cosmic microwave background) and increasingly in geography also uses FITS tables; this example shows how easy it is to include any meta-data you need (in this case, to turn row number into pixel position).

Before I'd invent a new data format, I'd simply use what others have been using very successfully for decades.   The additions needed for ImageJ are very modest (and would be good for totally other purposes).

Rick

On 27 Jul 2011, at 17:13, Terry L. Sprout wrote:

> Hello,
>
>
>
> I write scientific imaging software, which writes TIFF files to archive
> images. I recently added the ability to locate single photons in an
> image to sub-pixel accuracy. The software then uses the list of photons
> to create a new image that can be integrated for long exposures. When
> archiving these images, we only want to archive the list of photons and
> not the 2D image that is usually included in a TIFF file.
>
>
>
> I came up with a scheme that uses an IFD tag that I registered with
> Adobe. I want other TIFF readers to be able to use these files as well.
>
>
>
> I know others must have done this before and it might be best if I
> conform to existing schemes to make my files readable by other TIFF
> readers. Does anyone know of a scheme that is already being used? Is
> there an ImageJ plug-in for reading such files?
>
>
>
> I don't know much about what can be done with ImageJ. Can a developer
> extend the file formats used by ImageJ? In other words, can I write a
> plug-in to read these files of should someone from NIH extend the TIFF
> reader to read these files?
>
>
>
>
>
> Terry L. Sprout
>
> [phone]
>
> w7-32
>
>

[Terry L. Sprout]

Thank you Rick,

I agree with your comment about using known data formats before
inventing a new one. My customer wants TIFF, however, since we've been
doing TIFF for so long and there are lots of TIFF readers. Of course, it
doesn't help when none of those TIFF readers can read these files. I was
hoping someone knows of some existing data structures used in TIFF files
until we move to FITS (and I'm sure we will).


Terry L. Sprout
[phone]
w7-32

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Frederic V. Hessman
Sent: Wednesday, July 27, 2011 11:46 AM
To: [hidden email]
Subject: Re: Photon lists within TIFF files

This is a classic example of what FITS tables give you.  

You all may know of the simple FITS images supported by ImageJ, but the
standard actually supports much more complex data, including tabular
data (both as text and binary).   For example, most X-ray telescopes use
FITS tables, since their proportional counters do exactly what you're
doing: counting individual photons, their positions, and the times.  The
pixelation scheme called HEALPIX (which covers a sphere with equal area
diamonds at various resolutions) used by all-sky surveys like WMAP
(cosmic microwave background) and increasingly in geography also uses
FITS tables; this example shows how easy it is to include any meta-data
you need (in this case, to turn row number into pixel position).

Before I'd invent a new data format, I'd simply use what others have
been using very successfully for decades.   The additions needed for
ImageJ are very modest (and would be good for totally other purposes).

Rick

On 27 Jul 2011, at 17:13, Terry L. Sprout wrote:

> Hello,
>
>
>
> I write scientific imaging software, which writes TIFF files to
archive
> images. I recently added the ability to locate single photons in an
> image to sub-pixel accuracy. The software then uses the list of
photons
> to create a new image that can be integrated for long exposures. When
> archiving these images, we only want to archive the list of photons
and
> not the 2D image that is usually included in a TIFF file.
>
>
>
> I came up with a scheme that uses an IFD tag that I registered with
> Adobe. I want other TIFF readers to be able to use these files as
well.

>
>
>
> I know others must have done this before and it might be best if I
> conform to existing schemes to make my files readable by other TIFF
> readers. Does anyone know of a scheme that is already being used? Is
> there an ImageJ plug-in for reading such files?
>
>
>
> I don't know much about what can be done with ImageJ. Can a developer
> extend the file formats used by ImageJ? In other words, can I write a
> plug-in to read these files of should someone from NIH extend the TIFF
> reader to read these files?
>
>
>
>
>
> Terry L. Sprout
>
> [phone]
>
> w7-32
>
>